Biological invasions area a growing problem in South Africa. Many alien species have been introduced for various reasons and through multiple pathways over the past few centuries. Invasive alien reptiles and amphibians (herpetofauna) are not yet a major problem in the country. However, escalating difficulties with invasive species in these groups worldwide, and changing circumstances in South Africa, suggest a high risk of increased problems in the future. This paper reviews key issues pertaining to invasive alien herpetofauna worldwide and discusses how risk assessment can be used as part of an effective biosecurity strategy for South Africa. Nearly 300 species of alien herpetofauna have already been imported into the country via the pet trade and are being kept in captivity. There is a need to consider the potential threat of these species, and others still to be introduced, in line with practices in other countries where formal risk assessment policies are in place to separate potentially invasive species from those that are unlikely to be problematical. New legislation in South Africa seeks to regulate activities involving alien species, but exactly how this will be done has yet to be finalized. Each province in South Africa currently has its own legislation with different requirements; this causes many problems. Records of permit applications are also poor, complicating attempts to compile accurate inventories and to discern trends in imports and permit allocations. We define a pragmatic framework for dealing with alien reptiles and amphibians in South Africa. The framework identifies key issues facing the country and considers how the situation and advances elsewhere in the world can be used to set priorities. We propose that a risk assessment protocol be implemented for categorizing species as permissible or prohibited for import and trade. Accurate data are needed on the alien species already in South Africa.